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Fig. S1. Influence of the number of injected human CD34+ haematopoietic stem cells (HSC) on human cell chimerism in non-obese diabetic (NOD)-scid IL2rγnull- bone marrow, liver, thymus (NSG–BLT) mice. NSG mice were irradiated with 200 cGy (a,b) or non-irradiated (c,d) were implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space and then injected intravenously with the indicated number of CD34+ HSC derived from the autologous human CD3-depleted fetal liver. The peripheral blood of recipient NSG mice was screened for human CD45+ cell chimerism (a,c) and development of human CD3+ T cells (b,d) at 12 weeks after implant. Each point shown represents an individual mouse.

Fig. S2. Engraftment levels of human CD45+ cells in female or male non-obese diabetic (NOD)-scid IL2rγnull (NSG) mice implanted with tissues from either male or female donors. Male or female NSG mice were irradiated with 200 cGy, implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space and then injected intravenously with 1 × 105 to 5 × 105 CD34+ haematopoietic stem cells derived from the autologous human CD3-depleted fetal liver cells. Tissues both male (a) and female donors (b) were used. The peripheral blood of recipient NSG mice was screened for human CD45+ cell chimerism at 12 weeks after implant. Each letter on the x-axis represents a unique set of donor tissues and each point represents an individual mouse. *P < 0·05; **P < 0·01; ***P < 0·001.

Fig. S3. Thymocyte populations from non-obese diabetic (NOD)-scid IL2rγnull- bone marrow, liver, thymus (NSG–BLT) not irradiated and mice from each group were then implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space. All mice were then injected intravenously with 1 × 105 to 5 × 105 CD34+ haematopoietic stem cells derived from the autologous human CD3-depleted fetal liver. At 12 weeks post-implant, thymic tissues were recovered and the total number of CD45+ cells (a) and the proportion of CD4 and CD8 single-positive and double-positive cells (b) were determined using flow cytometry. **P < 0·001.

Fig. S4. Irradiation does not alter the activation status of human T cells in haematopoietic stem cells-engrafted non-obese diabetic (NOD)-scid IL2rγnull (NSG) mice implanted with human thymic tissues. NSG mice were irradiated with 200 cGy or not irradiated (0 cGy) and mice from each group were then implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space (thymic implant) or left unmanipulated (no thymic implant). All mice were then injected intravenously with 1 × 105 to 5 × 105 CD34+ haematopoietic stem cells derived from the autologous human CD3-depleted fetal liver. Human CD4+ T cells (a,b,c) and CD8+ T cells (d,e,f) were examined for the expression of CD45RA in the peripheral blood at 12 (a,d) and 16 (b,e) weeks and in the spleen at 16 weeks (c,f). The values shown represent the percentages of human CD4+ or CD8+ T cells expressing CD45RA. Data from NSG mice injected with human HSC in the absence of irradiation is not shown due to the very low levels of T cell development. Representative flow cytometry histograms for expression of CD45RA and CD62L on CD4+ (g,h) and CD8+ (i,j) T cells is shown for mice implanted with human fetal thymus and liver tissues. *P < 0·05; **P < 0·01; ***P < 0·001; ****P < 0·0001.

Fig. S5. Human CD4 and CD8 T cells from non-obese diabetic (NOD)-scid IL2rγnull-bone marrow, liver, thymus (NSG–BLT) mice produce cytokines following in-vitro stimulation.

NSG mice were either irradiated with 200 cGy or not irradiated and mice from each group were then implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space. All mice were then injected intravenously with 1 × 105 to 5 × 105 CD34+ haematopoietic stem cells derived from the autologous human CD3-depleted fetal liver. The ability of human CD4 T cells (a,c,e,g) and human CD8 T cells (b,d,f,h) from the spleens of mice from each group to produce interferon (IFN)-γ (a,b), interleukin (IL)-2 (c,d), IL-17A (e,f) and IL-22 (g,h) was determined at 12 weeks after tissue implant. Splenocytes were stimulated ex vivo with phorbol myristate acetate (PMA) and ionomycin for 5 h in a standard intracellular cytokine assay, as described in Materials and methods. *P < 0·05; ***P < 0·001.

Fig. S6. Irradiation does not alter human B cell maturation in non-obese diabetic (NOD)-scid IL2rγnull-bone marrow, liver, thymus (NSG–BLT) mice. NSG mice were either irradiated with 200 cGy or not irradiated (0 cGy) and mice from each group were then implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space. All mice were then injected intravenously with 1 × 105 to 5 × 105 CD34+ haematopoietic stem cells derived from the autologous human CD3-depleted fetal liver. Human B cell subsets were defined as follows: immature/transitional (CD10+/CD27/CD38+/IgD), transitional [CD10/CD27/CD38+/immunoglobulin (Ig)Ddim], naive (CD10/CD27/CD38/IgD+) and memory (CD10/CD27+) CD20+ B cells. The gating strategy used to identify the human B cell subsets is shown in (a). The proportion of immature/transitional (b), transitional (c), naive (d) and memory (e) CD20+ B cells is shown for the blood and spleen at 16 weeks post-implant and for human blood. *P < 0·05; **P < 0·01; ****P < 0·0001.

Fig. S7. Irradiation does not alter human innate immune cell development in non-obese diabetic (NOD)-scid IL2rγnull-bone marrow, liver, thymus (NSG–BLT) mice. NSG mice were irradiated with 200 cGy or not irradiated (0 cGy) and mice from each group were then implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space. All mice were then injected intravenously with 1 × 105 to 5 × 105 CD34+ haematopoietic stem cells derived from the autologous human CD3-depleted fetal liver. Human innate immune cell subsets were defined as follows: macrophage (CD14+/CD33+), myeloid dendritic cells (mDC, CD11c+/CD33+) and plasmacytoid dendritic cells (DC) (pDC, CD123+/CD33+). The gating strategy used to identify the human innate subsets is shown in (a). The proportion of monocyte/macrophage (b), mDC (c) and pDC (d) is shown for the blood, spleen and bone marrow at 16 weeks post-implant and for human blood. **P < 0·01; ***P < 0·001.

Fig. S8. Influence of the number of injected human CD34+ haematopoietic stem cells (HSC) and T cell levels on the incidence of xeno-graft-versus-host disease (GVHD) in non-obese diabetic (NOD)-scid IL2rγnull-bone marrow, liver, thymus (NSG–BLT) mice. NSG mice were irradiated with 200 cGy and implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space and then injected intravenously with the indicated number of CD34+ HSC derived from the autologous human CD3-depleted fetal liver. (a) NSG–BLT mice were monitored for survival and the day of death compared to the number of injected HSC is shown. (b) The peripheral blood of recipient NSG mice was screened for development of human CD3+ T cells at 12 weeks after implant and compared to the day of death. (c) The incidence of GVHD was also compared for male NSG mice engrafted with either female or male donor tissues. Each point shown represents an individual mouse. Survival was monitored over 200 days after implant.

Fig. S9. Comparison of human chimerism levels in individual cohorts of non-obese diabetic (NOD)-scid IL2rγnull(NSG) mice implanted with fetal tissues from the same donors.

NSG mice were irradiated with 200 cGy or not irradiated (0 cGy) and mice from each group were then implanted with 1 mm3 fragments of human fetal thymus and liver in the renal subcapsular space (thymic implant) or left unmanipulated (no thymic implant). All mice were then injected intravenously with 1 × 105 to 5 × 105 CD34+ haematopoietic stem cells derived from the autologous human CD3-depleted fetal liver. At 12 weeks (a,b,c) and 16 weeks (d,e,f) after implant, the peripheral blood of recipient NSG mice was screened for human CD45+ cell chimerism (a,d), T cell development (b,e) and B cell development (c,f). Each colour represents a unique set of donor tissues, and each symbol type indicates the specific implant protocol used to generate the mice. Each point represents an individual mouse.

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